Turned on overlap ratio resolver

jts · Jan 14, 2013 · 2dc5e59 · 2dc5e59
1 parent 653ce21
commit 2dc5e59
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Showing 3 changed files with 10 additions and 4 deletions.
diff --git a/src/Algorithm/ErrorCorrectProcess.cpp b/src/Algorithm/ErrorCorrectProcess.cpp
@@ -41,8 +41,7 @@ ErrorCorrectResult ErrorCorrectProcess::process(const SequenceWorkItem& workItem
 
 ErrorCorrectResult ErrorCorrectProcess::correct(const SequenceWorkItem& workItem)
 {
-    /*
-    ErrorCorrectResult iresult = fmiCorrect(workItem, 31);
+    ErrorCorrectResult iresult = fmiCorrect(workItem, 25);
     if(!iresult.kmerQC)
     {
         //std::cout << "KMER\n";
@@ -53,7 +52,7 @@ ErrorCorrectResult ErrorCorrectProcess::correct(const SequenceWorkItem& workItem
         //std::cout << "FMI\n";
         return iresult;
     }
-    */
+
     switch(m_params.algorithm)
     {
         case ECA_HYBRID:

diff --git a/src/Algorithm/ErrorCorrectProcess.h b/src/Algorithm/ErrorCorrectProcess.h
@@ -19,6 +19,7 @@
 #include "BWTIndexSet.h"
 #include "SampledSuffixArray.h"
 #include "multiple_alignment.h"
+#include "BloomFilter.h"
 
 enum ErrorCorrectAlgorithm
 {
@@ -44,6 +45,7 @@ struct ErrorCorrectParameters
     //
     const OverlapAlgorithm* pOverlapper;
     BWTIndexSet indices;
+    BloomFilter* pBloomFilter;
     bool trim;
 
     // Overlap-based corrector params

diff --git a/src/SGA/assemble.cpp b/src/SGA/assemble.cpp
@@ -224,7 +224,12 @@ void assemble()
             pGraph->visit(smoothingVisit);
         pGraph->simplify();
     }
-
+
+    // Resolve repeats by overlap length    
+    SGOverlapRatioVisitor ratioVisit(0.7);
+    pGraph->visit(ratioVisit);
+    pGraph->simplify();
+
     pGraph->renameVertices("contig-");
 
     std::cout << "\n[Stats] Final graph:\n";